B b @s4dZddlmZGdddeZddZddZd S) z5Parse Cluster Buster position frequency matrix files.)motifsc@seZdZdZddZdS)RecordzClass to store the information in a Cluster Buster matrix table. The record inherits from a list containing the individual motifs. cCsddd|DS)N css|]}t|VqdS)N)str).0motifr7lib/python3.7/site-packages/Bio/motifs/clusterbuster.py sz!Record.__str__..)join)selfrrr __str__szRecord.__str__N)__name__ __module__ __qualname____doc__r rrrr r srcsd}t}ggggdd}x|D]}|}|r"|dr|dkrbtjdd}||_|||dd}ggggd|d7}q"|d rq"|}t|d kr"fd d t d dddg|Dq"Wtjdd}||_|||S)zRead motifs in Cluster Buster position frequency matrix format from a file handle. Cluster Buster motif format: http://zlab.bu.edu/cluster-buster/help/cis-format.html r)ACGT>ZGATC)ZalphabetcountsN#cs"g|]\}}|t|qSr)appendfloat)rZ nucleotideZnucleotide_count)nucleotide_countsrr 5szread..rrrr) rstrip startswithrZMotifnamersplitlenzip)ZhandleZ motif_nbrrecordZ motif_namelinerZmatrix_columnsr)rr reads4        r(cCsxg}xd|D]\}d|jd}||x>t|jd|jd|jd|jdD]}|dj|qNWq Wd|}|S) zWReturn the representation of motifs in Cluster Buster position frequency matrix format.rrrrrrz {:0.0f} {:0.0f} {:0.0f} {:0.0f} r)r"rr%rformatr )rlinesmr'Z ACGT_countstextrrr writeBs  ( r-N)rZBiorlistrr(r-rrrr s  ,